public override SortedMaxSizedContainer <PeptideSpectralMatch> Search(IMassSpectrum spectrum, IEnumerable <Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer <PeptideSpectralMatch> results = new SortedMaxSizedContainer <PeptideSpectralMatch>(MaxMatchesPerSpectrum);
double[] eMasses = spectrum.MassSpectrum.GetMasses();
double[] eIntenisties = spectrum.MassSpectrum.GetIntensities();
double tic = spectrum.MassSpectrum.GetTotalIonCurrent();
;
foreach (var peptide in peptides)
{
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType)
{
Peptide = peptide
};
double[] tMasses =
peptide.Fragment(fragmentTypes)
.Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1))
.OrderBy(val => val)
.ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
results.Add(psm);
}
return(results);
}
public void SortedMaxSizedContainerMaxSizeNotExceeded()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
1, 2, 3, 4, 5, 6, 7
};
Assert.AreEqual(container.Count, container.MaxSize);
}
public void SortedMaxSizedContainerRemoveExistentItem()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
7, 6, 5, 4, 3, 2, 1
};
Assert.IsTrue(container.Remove(3));
}
public void SortedMaxSizedContainerDoesNotContainsItem()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
7, 6, 5, 4, 3, 2, 1
};
Assert.IsFalse(container.Contains(7));
}
public void SortedMaxSizedContainerContainsItem()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
7, 6, 5, 4, 3, 2, 1
};
Assert.IsTrue(container.Contains(3));
}
public void SortedMaxSizedContainerAddDefaultItem()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
0, 0, 0, 0, 0, 0, 0, 0
};
Assert.AreEqual(container.Count, 5);
}
public void SortedMaxSizedContainerRemoveExistentItemProperCount()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
7, 6, 5, 4, 3, 2, 1
};
container.Remove(3);
Assert.AreEqual(container.Count, 4);
}
public void SortedMaxSizedContainerRemoveExistentItemDoesntContain()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
7, 6, 5, 4, 3, 2, 1
};
container.Remove(3);
Assert.IsFalse(container.Contains(3));
}
public void SortedMaxSizedContainerClear()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
1, 2, 3
};
container.Clear();
Assert.AreEqual(container.Count, 0);
}
public void SortedMaxSizedContainerOnlySmallestItemsRemain()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
7, 6, 5, 4, 3, 2, 1
};
int[] data = container.ToArray();
Assert.AreEqual(data, new[] { 1, 2, 3, 4, 5 });
}
public void SortedMaxSizedContainerClearMaxSizeUneffected()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
1, 2, 3
};
container.Clear();
Assert.AreEqual(container.MaxSize, 5);
}
public void SortedMaxSizedContainerInverseComparer()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5, Comparer <int> .Create((a, b) => b.CompareTo(a)))
{
7, 6, 5, 4, 3, 2, 1
};
int[] data = container.ToArray();
Assert.AreEqual(data, new[] { 7, 6, 5, 4, 3 });
}
public void SortedMaxSizedContainerRemoveFirstItemCorrectCollection()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
7, 6, 5, 4, 3, 2, 1
};
container.Remove(1);
int[] data = container.ToArray();
Assert.AreEqual(data, new[] { 2, 3, 4, 5 });
}
public void SortedMaxSizedContainerLargeRemoveCount()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(25);
for (int i = 0; i < 30; i++)
{
container.Add(i);
}
container.Remove(17);
Assert.AreEqual(container.Count, 24);
}
public void SortedMaxSizedContainerLargeRemove()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(25);
for (int i = 0; i < 30; i++)
{
container.Add(i);
}
Assert.IsTrue(container.Remove(17));
}
public void SortedMaxSizedContainerLarge()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(25);
for (int i = 0; i < 30; i++)
{
container.Add(i);
}
Assert.AreEqual(container.Count, 25);
}
public void SortedMaxSizedContainerRemoveDuplicateItemCorrectCollection()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5)
{
1, 1, 1, 1, 1, 1, 1
};
container.Remove(1);
int[] data = container.ToArray();
Assert.AreEqual(data, new[] { 1, 1, 1, 1 });
}
public virtual SortedMaxSizedContainer <PeptideSpectralMatch> Search(IMassSpectrum massSpectrum, IEnumerable <Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer <PeptideSpectralMatch> results = new SortedMaxSizedContainer <PeptideSpectralMatch>(MaxMatchesPerSpectrum);
foreach (var peptide in peptides)
{
results.Add(Search(massSpectrum, peptide, fragmentTypes, productMassTolerance));
}
return(results);
}
public void Read(IList <Modification> fixedModifications, int numberOfTopHits = 1, bool higherScoresAreBetter = false)
{
_data.Clear();
bool first = true;
using (CsvReader reader = new CsvReader(new StreamReader(FilePath), true))
{
string[] headers = reader.GetFieldHeaders();
HasPPMInfo = headers.Contains("Precursor Mass Error (ppm)");
while (reader.ReadNextRecord())
{
if (first)
{
RawFileName = reader["Filename/id"].Split('.')[0];
first = false;
}
int scanNumber = int.Parse(reader["Spectrum number"]);
PSM psm = new PSM(scanNumber)
{
Score = double.Parse(reader["E-value"])
};
SortedMaxSizedContainer <PSM> peptides;
if (!_data.TryGetValue(scanNumber, out peptides))
{
peptides = new SortedMaxSizedContainer <PSM>(numberOfTopHits);
_data.Add(scanNumber, peptides);
}
if (!peptides.Add(psm))
{
continue;
}
psm.FileName = reader["Filename/id"];
psm.Charge = int.Parse(reader["Charge"]);
psm.IsDecoy = reader["Defline"].StartsWith("DECOY_");
if (HasPPMInfo)
{
psm.PrecursorMassError = double.Parse(reader["Precursor Mass Error (ppm)"]);
}
psm.SetSequenceAndMods(reader["Peptide"].ToUpper(), fixedModifications, reader["Mods"]);
}
}
PeptideSpectralMatches.Clear();
foreach (SortedMaxSizedContainer <PSM> set in _data.Values)
{
PeptideSpectralMatches.AddRange(set);
}
}
public void SortedMaxSizedContainerLargeRemoveEach()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(25);
for (int i = 0; i < 30; i++)
{
container.Add(i);
}
for (int i = 0; i < 25; i++)
{
container.Remove(i);
}
Assert.AreEqual(container.Count, 0);
}
public override SortedMaxSizedContainer<PeptideSpectralMatch> Search(IMassSpectrum spectrum, IEnumerable<Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer<PeptideSpectralMatch> results = new SortedMaxSizedContainer<PeptideSpectralMatch>(MaxMatchesPerSpectrum);
double[] eMasses = spectrum.MassSpectrum.GetMasses();
double[] eIntenisties = spectrum.MassSpectrum.GetIntensities();
double tic = spectrum.MassSpectrum.TotalIonCurrent;
foreach (var peptide in peptides)
{
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType) {Peptide = peptide};
double[] tMasses =
peptide.Fragment(fragmentTypes)
.Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1))
.OrderBy(val => val)
.ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
results.Add(psm);
}
return results;
}
public void SortedMaxSizedContainerRemoveNonExistentItem()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 7, 6, 5, 4, 3, 2, 1 };
Assert.IsFalse(container.Remove(7));
}
public void SortedMaxSizedContainerRemoveExistentItemProperCount()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 7, 6, 5, 4, 3, 2, 1 };
container.Remove(3);
Assert.AreEqual(container.Count, 4);
}
public void SortedMaxSizedContainerMaxSize()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5);
Assert.AreEqual(container.MaxSize, 5);
}
public void SortedMaxSizedContainerLarge()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(25);
for (int i = 0; i < 30; i++)
container.Add(i);
Assert.AreEqual(container.Count, 25);
}
public void SortedMaxSizedContainerDoesNotContainsItem()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 7, 6, 5, 4, 3, 2, 1 };
Assert.IsFalse(container.Contains(7));
}
public void SortedMaxSizedContainerContainsItem()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 7, 6, 5, 4, 3, 2, 1 };
Assert.IsTrue(container.Contains(3));
}
public void SortedMaxSizedContainerClear()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 1, 2, 3 };
container.Clear();
Assert.AreEqual(container.Count, 0);
}
public void SortedMaxSizedContainerLargeRemove()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(25);
for (int i = 0; i < 30; i++)
container.Add(i);
Assert.IsTrue(container.Remove(17));
}
public void Read(IList<Modification> fixedModifications, int numberOfTopHits = 1, bool higherScoresAreBetter = false)
{
_data.Clear();
bool first = true;
using (CsvReader reader = new CsvReader(new StreamReader(FilePath), true))
{
string[] headers = reader.GetFieldHeaders();
HasPPMInfo = headers.Contains("Precursor Mass Error (ppm)");
while (reader.ReadNextRecord())
{
if (first)
{
RawFileName = reader["Filename/id"].Split('.')[0];
first = false;
}
int scanNumber = int.Parse(reader["Spectrum number"]);
PSM psm = new PSM(scanNumber) {Score = double.Parse(reader["E-value"])};
SortedMaxSizedContainer<PSM> peptides;
if (!_data.TryGetValue(scanNumber, out peptides))
{
peptides = new SortedMaxSizedContainer<PSM>(numberOfTopHits);
_data.Add(scanNumber, peptides);
}
if (!peptides.Add(psm))
continue;
psm.FileName = reader["Filename/id"];
psm.Charge = int.Parse(reader["Charge"]);
psm.IsDecoy = reader["Defline"].StartsWith("DECOY_");
if (HasPPMInfo)
psm.PrecursorMassError = double.Parse(reader["Precursor Mass Error (ppm)"]);
psm.SetSequenceAndMods(reader["Peptide"].ToUpper(), fixedModifications, reader["Mods"]);
}
}
PeptideSpectralMatches.Clear();
foreach (SortedMaxSizedContainer<PSM> set in _data.Values)
{
PeptideSpectralMatches.AddRange(set);
}
}
public void UpdatePsmInformation(MSDataFile dataFile, bool is2dFDR = true, bool useMedian = true, double evalueThreshold = 1e-3)
{
List <double> errors = new List <double>();
MaximumPrecursorMassError = 0;
int count = 0;
int msms = 0;
int ms = 0;
int localMSMS = -1;
List <int> msmsBetweenMS = new List <int>();
List <double> injectionTimes = new List <double>();
for (int sn = dataFile.FirstSpectrumNumber; sn <= dataFile.LastSpectrumNumber; sn++)
{
int order = dataFile.GetMsnOrder(sn);
if (order == 1)
{
ms++;
if (localMSMS >= 0)
{
msmsBetweenMS.Add(localMSMS);
}
localMSMS = 0;
}
else
{
localMSMS++;
msms++;
injectionTimes.Add(dataFile.GetInjectionTime(sn));
}
}
MaxMSMSScansBetweenMS = msmsBetweenMS.Max();
AverageMSMSSCansBetweenMS = msmsBetweenMS.Average();
TotalMSMSscans = msms;
TotalMSscans = ms;
AverageMSMSInjectionTime = injectionTimes.Average();
MaxMSMSInjectionTime = injectionTimes.Max();
foreach (KeyValuePair <int, SortedMaxSizedContainer <PSM> > kvp in _data)
{
int scanNumber = kvp.Key;
SortedMaxSizedContainer <PSM> psms = kvp.Value;
double isolationMZ = dataFile.GetPrecusorMz(scanNumber);
Polarity polarity = dataFile.GetPolarity(scanNumber);
foreach (PSM psm in psms)
{
psm.Charge *= (int)polarity; // For negative mode ions
psm.IsolationMz = isolationMZ;
double isolationMass = Mass.MassFromMz(isolationMZ, psm.Charge);
double theoreticalMass = psm.MonoisotopicMass;
int nominalMassOffset;
double adjustedIsolationMass;
Tolerance tolerancePPM = Tolerance.CalculatePrecursorMassError(theoreticalMass,
isolationMass, out nominalMassOffset, out adjustedIsolationMass);
psm.AdjustedIsolationMass = adjustedIsolationMass;
psm.IsotopeSelected = nominalMassOffset;
if (!HasPPMInfo)
{
psm.PrecursorMassError = tolerancePPM.Value;
}
double positive = Math.Abs(psm.PrecursorMassError);
if (positive > MaximumPrecursorMassError)
{
MaximumPrecursorMassError = positive;
}
if (psm.FdrScoreMetric <= evalueThreshold)
{
errors.Add(psm.PrecursorMassError);
}
count++;
}
}
SystematicPrecursorMassError = useMedian ? GetMedianValue(errors) : errors.Average();
// Adjust all psms to
foreach (PSM psm in PeptideSpectralMatches)
{
psm.CorrectedPrecursorMassError = psm.PrecursorMassError - SystematicPrecursorMassError;
}
}
public void SortedMaxSizedContainerRemoveNonExistentItemCorrectCollection()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 7, 6, 5, 4, 3, 2, 1 };
container.Remove(8);
int[] data = container.ToArray();
Assert.AreEqual(data, new[] { 1, 2, 3, 4, 5 });
}
public void SortedMaxSizedContainerMaxSize()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5);
Assert.AreEqual(container.MaxSize, 5);
}
public void SortedMaxSizedContainerAddDefaultItem()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 0, 0, 0, 0, 0, 0, 0, 0 };
Assert.AreEqual(container.Count, 5);
}
public void SortedMaxSizedContainerMaxSizeNotExceeded()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 1, 2, 3, 4, 5, 6, 7 };
Assert.AreEqual(container.Count, container.MaxSize);
}
public void SortedMaxSizedContainerClearMaxSizeUneffected()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 1, 2, 3 };
container.Clear();
Assert.AreEqual(container.MaxSize, 5);
}
public void SortedMaxSizedContainerOnlySmallestItemsRemain()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 7, 6, 5, 4, 3, 2, 1 };
int[] data = container.ToArray();
Assert.AreEqual(data, new[] { 1, 2, 3, 4, 5 });
}
public void SortedMaxSizedContainerCountIntiallyZero()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5);
Assert.AreEqual(container.Count, 0);
}
public void SortedMaxSizedContainerRemoveDuplicateItemCorrectCollection()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 1, 1, 1, 1, 1, 1, 1 };
container.Remove(1);
int[] data = container.ToArray();
Assert.AreEqual(data, new[] { 1, 1, 1, 1 });
}
public void SortedMaxSizedContainerInverseComparer()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5, Comparer<int>.Create((a, b) => b.CompareTo(a))) { 7, 6, 5, 4, 3, 2, 1 };
int[] data = container.ToArray();
Assert.AreEqual(data, new[] { 7, 6, 5, 4, 3 });
}
public void SortedMaxSizedContainerRemoveExistentItemDoesntContain()
{
SortedMaxSizedContainer<int> container = new SortedMaxSizedContainer<int>(5) { 7, 6, 5, 4, 3, 2, 1 };
container.Remove(3);
Assert.IsFalse(container.Contains(3));
}
public virtual SortedMaxSizedContainer<PeptideSpectralMatch> Search(IMassSpectrum massSpectrum, IEnumerable<Peptide> peptides, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
SortedMaxSizedContainer<PeptideSpectralMatch> results = new SortedMaxSizedContainer<PeptideSpectralMatch>(MaxMatchesPerSpectrum);
foreach (var peptide in peptides)
{
results.Add(Search(massSpectrum, peptide, fragmentTypes, productMassTolerance));
}
return results;
}
public void SortedMaxSizedContainerCountIntiallyZero()
{
SortedMaxSizedContainer <int> container = new SortedMaxSizedContainer <int>(5);
Assert.AreEqual(container.Count, 0);
}
